Background: Apple fruits are rich in flavonoids, and play important roles in human-health protection against chronic diseases. However, pitter pit in apple has affected apple fruit production worldwide. There must be some application values could be exploited from the bitter-pit apples so as to reduce the loss caused by bitter pit.Results: In the present study, the influence of bitter pit on the total flavonoid content and flavonoid biosynthesis in apples was investigated using the aluminum chloride colorimetric method, whole-transcriptome sequencing and qRT-PCR analysis. The results showed that the total flavonoid content in bitter-pit apples (BG), pitted parts (BGBB) and non-pitted parts (JKBF) was 4.28-fold, 4.68-fold and 0.57-fold respectively as that in healthy apples (JKG). By RNA-Seq analysis, 26, 23 and 3 DEGs involved in flavonoid biosynthesis were enriched in JKG vs. BG, JKG vs. BGBB and JKG vs. JKBF comparisons, respectively. Eight DEGs [CYP98A3(1), CYP98A3(2), BADH, DAT, HCT(1), HCT(2), CHI(1) and CHI(2)], were selected to be validated by qRT-PCR analysis, and the consistent expression patterns with RNA-Seq analysis were obtained, the results showed that the 8 DEGs were upregulated in BG and BGBB but downregulated in JKBF when compared with JKG.Conclusions: The flavonoid accumulation and biosynthesis in apples, especially the pitted parts, were stimulated greatly by bitter pit, while depressed slightly in non-pitted parts. The results indicated that the bitter-pit apples, especially the pitted parts, could be used as the promising bioresource of total flavonoid for the therapeutic utilization in human chronic diseases.